Re: [galaxy-dev] Tools pick up Python modules from Galaxy core rather than installed tool dependencies

2016-12-20 Thread Peter Briggs
ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 From: Nate Coraor [n...@bx.psu.edu] Sent: Monday, December 19, 2016 5:50 PM To: Peter Briggs Cc: Galaxy Dev List Subject: Re: [galaxy-dev] Tools pick up Python mo

Re: [galaxy-dev] Tools pick up Python modules from Galaxy core rather than installed tool dependencies

2016-12-19 Thread Nate Coraor
Hi Peter, Thanks for posting your findings. You can also directly manipulate the PYTHONPATH in tags in job_conf.xml s, which may be enough, although this would be tedious for every dependency. --nate On Fri, Dec 16, 2016 at 5:35 AM, Peter Briggs wrote: > I think I've figured this out in the e

Re: [galaxy-dev] Tools pick up Python modules from Galaxy core rather than installed tool dependencies

2016-12-16 Thread Peter Briggs
I think I've figured this out in the end, posting my solution in case anyone else comes across it in future. The issue was due to a change in the way that Python setuptools adds its installed modules to the search path (sys.path) via easy-install.pth files. Later versions of setuptools (>=25.0.